Amp design logic

The price of anything is always what someone is willing to pay for it. A $50K amp that has never been sold is not worth $50K, it is really quite simple.
OTOH some of the "best" parts prices (called components by manufacturers BTW) are higher than you might imagine . Look up Deuland capacitors for instance and think of multiples of that cost.
Labor/benefits costs also seems to matter greatly. I needn't tell you that some populus countries that are making most of the consumer electronics now, have very low costs. In fact all overhead costs energy, space etc. vary widely by place of manufacture.
Many things we covet are kept intentionally scarce and never marked down these have a quote a pride of ownership cost assiciated (Think Patek Phillipe, Cartier, ST DuPont) etc.) Certainly this phenomena is part of this hobby.
Don't forget patented proprietary circuit designs. A lot of manufacturers do not release diagrams (schematics) and code parts with their own numbers, making duplcation and reverse engineering very difficult.
Well that is a start but when you finish your perfectly built DIY $50K, for only ?$1K?? let us all know if it sounds as good as the original.
But in the end only the demand will ultimately decide the price.

So the parts (I am guessing) are 10% and a retailer marks up double in most cases. How much is the manufacturers and distributors profit? Isn't overhead part of construction costs?

You can't turn a Volkswagon into Bugatti, but you can alter/modify cars to excel at specific purposes. I think it is obvious that cars used in many races are based upon street models but have many parts changed/exchanged to upgrade performance.
Their is a thriving industry in this hobby living off the same idea. I can hardly think of any component that hasn't been or can't be modified. I myself can do little beyond rolling tubes, but I do that with some zeal, and I have employed others to mod a few pieces.
Some people do claim that modified components make their gear the equivalent of something much more costly. In any event it is abundantly clear that their is a strong belief in the value of modification.